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Don't believe me? Well, let's look at some numbers and facts. The 49ers have given up 260 points in eight games this season, and that's with a shutout in Week 1. That would mean the team is on pace to give up 520 points overall, which averages out to 32.5 per game. If you look at their last seven games, the total actually goes up to 37 points per contest. So if things stay status quo, San Francisco will probably allow something closer to 550 points this season.
Looking deeper into the overall horribleness, the 49ers are currently on pace to give up 3,088 yards rushing, which would be the most in the NFL since the 1978 Buffalo Bills. They've given up 240 yards or more on the ground in three straight games, which no team has done since the 1977 Kansas City Chiefs. Also, per Elias Sports, they are the only team to allow a 100-yard rusher in seven straight games.
San Francisco has done all of this despite drafting heavily on defense the past four years. Since 2013, general manager Trent Baalke has used 10 of a possible 15 picks in rounds 1-3 on defensive players. If you break those selections down, he's taken three defensive linemen (Tank Carradine, Arik Armstead, DeForest Buckner), three linebackers (Corey Lemonier, Chris Borland, Eli Harold), two cornerbacks (Jimmie Ward, Will Redmond), and two safeties (Eric Reid, Jaquiski Tartt). It's a pretty balanced approach in terms of positions, and eight of those players are still on the roster (Lemonier and Borland being the exceptions). When you look at guys like Buckner, Armstead, Ward, and Tartt, and add in other young talents like Aaron Lynch and Rashard Robinson, it almost looks like the Niners have some nice building blocks on paper.
So what's the problem? Well, there is that whole issue of coaching, and believe me, the employment of defensive coordinator Jim O'Neil is a cause for concern. The hire was a curious one, to begin with, as O'Neil's two years in the same position with the Cleveland Browns weren't anything to write home about. In 2014, the Brown's secondary played well enough, but the run defense was last in the league with 2,265 yards allowed. The following season, head coach Mike Pettine stepped away from his role with the defense and gave the reigns totally to O'Neil. The results were disastrous as the Browns quickly descended towards the bottom of the NFL in most major defensive categories including points allowed, total yards allowed, and yards per play. The issues with the run defense also remained, as the Browns finished 29th, once again allowing over 2,000 yards (2,055). Also notable under O'Neil was the lack of development from younger players, something that's held true in San Francisco.
Rather than being assigned specific gaps, Cleveland's defensive linemen play different techniques based on how their offensive counterparts are blocking them. The linebackers, then, are expected to guess what technique their teammates are using, scrape through the resulting mess and make the play. Opposing offenses have identified this flaw on film and are repeatedly, week-after-week, gashing the edge of Cleveland's defense. It's a completely chaotic approach to stopping the run, and players have said—off the record—they're spending way too much time thinking, and not nearly enough time reacting.
This is basically an issue with gap integrity, something O'Neil has admitted he's not familiar with. When asked in a press conference how he would assess the gap integrity along his defensive line, O'Neil's response was, "I don't know what you mean by that." Meanwhile, the defense has been destroyed on the ground week after week with no end in sight.
Despite the issues at hand, head coach Chip Kelly has repeatedly said that he's not making any changes to his defensive staff. While it's understandable that Kelly wants to stay loyal to his coaches, continuing to employ O'Neil at this point is bordering on insanity. The maligned coordinator's confusing scheme isn't doing San Francisco's young defensive building blocks any favors, and at this point, you'd have to wonder if it's stunted their development.
What's most maddening is that even if the team relieved O'Neil of his duties now, there isn't really anyone else on the staff you could see as a long-term answer. Senior Defensive Assistant Jason Tarver has experience as a coordinator, but his time running the show in Oakland with the Raiders from 2012-2014 was a disaster. His units never finished better than 29th overall in total defense. Combine that with the fact that many defensive coaches steer clear from Kelly because of his fast-paced scheme, and the answer isn't clear right now. Still, even if the 49ers had to finish out the year with Tarver and get creative in the offseason (if Kelly's still around) it's better than the alternative. O'Neil has to go, and he has to go now.
